So this is what I'm going to do, or at least plan to do. Because the trench sidewalls install on the lower hull you can drill and add fibers all day long with nary a worry. Like you said the problem comes when you try to put the upper hull on, you have that "inside" wall that will shear them off above the mating surfaces. My plan is to grind away the majority of the inside wall on the upper hull, leaving sections (like teeth) that will fit between the higher fibers that can then be glued to the lower hulls inside wall. I have used, back and forth, Tamiya Extra Thin cement and Model Master liquid cement (the one with the metal tube) and both work great on the Zvezda plastic. Because the MM glue is a wee bit thicker I can place a drop on the bottom of the upper hull teeth and lower the upper hull onto the lower hull before the glue evaporates. I don't plan on a million fibers in the trench so there should be plenty of mating surface left after removing material from the upper hull inner wall.
Did I explain that good? It sounds plausible in my head, LOL.